Multiple sequence alignment - TraesCS1B01G118800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G118800 chr1B 100.000 2480 0 0 1 2480 139482591 139480112 0.000000e+00 4580.0
1 TraesCS1B01G118800 chr1A 84.757 1686 147 57 109 1740 82154075 82152446 0.000000e+00 1589.0
2 TraesCS1B01G118800 chr1A 90.826 109 8 2 2018 2125 82149005 82148898 7.150000e-31 145.0
3 TraesCS1B01G118800 chr1D 90.123 1053 57 15 805 1811 86784033 86782982 0.000000e+00 1325.0
4 TraesCS1B01G118800 chr1D 85.569 589 48 19 1906 2480 86782695 86782130 1.280000e-162 582.0
5 TraesCS1B01G118800 chr1D 83.577 274 31 7 542 803 477491181 477490910 6.850000e-61 244.0
6 TraesCS1B01G118800 chr1D 88.889 54 3 3 333 386 86784882 86784832 2.060000e-06 63.9
7 TraesCS1B01G118800 chr5B 89.778 225 18 4 2258 2480 699384980 699385201 1.450000e-72 283.0
8 TraesCS1B01G118800 chr5B 83.835 266 33 5 539 803 694528417 694528673 6.850000e-61 244.0
9 TraesCS1B01G118800 chr3B 85.662 272 31 5 539 803 360008105 360008375 1.880000e-71 279.0
10 TraesCS1B01G118800 chr2A 83.860 285 25 8 539 803 235327738 235328021 4.090000e-63 252.0
11 TraesCS1B01G118800 chr2A 94.286 105 6 0 1 105 21661941 21661837 7.100000e-36 161.0
12 TraesCS1B01G118800 chr4D 84.000 275 27 7 542 803 336117466 336117196 5.300000e-62 248.0
13 TraesCS1B01G118800 chr4D 95.098 102 5 0 1 102 274513787 274513686 7.100000e-36 161.0
14 TraesCS1B01G118800 chr3D 81.655 278 26 10 542 804 124535011 124534744 8.990000e-50 207.0
15 TraesCS1B01G118800 chr3D 95.192 104 4 1 3 105 115090565 115090462 1.970000e-36 163.0
16 TraesCS1B01G118800 chr4B 84.746 177 21 6 2141 2314 658580425 658580598 3.280000e-39 172.0
17 TraesCS1B01G118800 chr5D 82.243 214 23 5 544 746 473341090 473341299 1.180000e-38 171.0
18 TraesCS1B01G118800 chr5D 93.043 115 8 0 1 115 175270558 175270444 4.240000e-38 169.0
19 TraesCS1B01G118800 chr6B 96.078 102 4 0 1 102 665155904 665156005 1.530000e-37 167.0
20 TraesCS1B01G118800 chr4A 96.000 100 4 0 3 102 491670630 491670531 1.970000e-36 163.0
21 TraesCS1B01G118800 chr2D 96.000 100 4 0 3 102 62350488 62350389 1.970000e-36 163.0
22 TraesCS1B01G118800 chr7D 95.098 102 5 0 1 102 431155811 431155710 7.100000e-36 161.0
23 TraesCS1B01G118800 chr3A 95.098 102 5 0 1 102 475931726 475931827 7.100000e-36 161.0
24 TraesCS1B01G118800 chr6A 90.756 119 10 1 538 656 522643887 522643770 9.180000e-35 158.0
25 TraesCS1B01G118800 chr6D 86.747 83 5 4 539 615 470905797 470905879 1.220000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G118800 chr1B 139480112 139482591 2479 True 4580.000000 4580 100.000000 1 2480 1 chr1B.!!$R1 2479
1 TraesCS1B01G118800 chr1A 82148898 82154075 5177 True 867.000000 1589 87.791500 109 2125 2 chr1A.!!$R1 2016
2 TraesCS1B01G118800 chr1D 86782130 86784882 2752 True 656.966667 1325 88.193667 333 2480 3 chr1D.!!$R2 2147

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
390 391 0.100503 GTTGGTTCCATATGCGTGCC 59.899 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 6144 0.104671 CCACAACACCCAGCAAAAGG 59.895 55.0 0.0 0.0 0.0 3.11 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.963383 CCGCTAGGTTTATTTCGCATT 57.037 42.857 0.00 0.00 0.00 3.56
31 32 4.287238 CCGCTAGGTTTATTTCGCATTT 57.713 40.909 0.00 0.00 0.00 2.32
32 33 5.412526 CCGCTAGGTTTATTTCGCATTTA 57.587 39.130 0.00 0.00 0.00 1.40
33 34 5.997385 CCGCTAGGTTTATTTCGCATTTAT 58.003 37.500 0.00 0.00 0.00 1.40
34 35 6.435428 CCGCTAGGTTTATTTCGCATTTATT 58.565 36.000 0.00 0.00 0.00 1.40
35 36 6.577427 CCGCTAGGTTTATTTCGCATTTATTC 59.423 38.462 0.00 0.00 0.00 1.75
36 37 7.129622 CGCTAGGTTTATTTCGCATTTATTCA 58.870 34.615 0.00 0.00 0.00 2.57
37 38 7.642194 CGCTAGGTTTATTTCGCATTTATTCAA 59.358 33.333 0.00 0.00 0.00 2.69
38 39 8.958043 GCTAGGTTTATTTCGCATTTATTCAAG 58.042 33.333 0.00 0.00 0.00 3.02
39 40 7.755582 AGGTTTATTTCGCATTTATTCAAGC 57.244 32.000 0.00 0.00 0.00 4.01
40 41 6.756542 AGGTTTATTTCGCATTTATTCAAGCC 59.243 34.615 0.00 0.00 0.00 4.35
41 42 6.756542 GGTTTATTTCGCATTTATTCAAGCCT 59.243 34.615 0.00 0.00 0.00 4.58
42 43 7.918562 GGTTTATTTCGCATTTATTCAAGCCTA 59.081 33.333 0.00 0.00 0.00 3.93
43 44 9.296400 GTTTATTTCGCATTTATTCAAGCCTAA 57.704 29.630 0.00 0.00 0.00 2.69
44 45 9.862371 TTTATTTCGCATTTATTCAAGCCTAAA 57.138 25.926 0.00 0.00 0.00 1.85
45 46 9.862371 TTATTTCGCATTTATTCAAGCCTAAAA 57.138 25.926 0.00 0.00 0.00 1.52
46 47 7.575332 TTTCGCATTTATTCAAGCCTAAAAC 57.425 32.000 0.00 0.00 0.00 2.43
47 48 5.328691 TCGCATTTATTCAAGCCTAAAACG 58.671 37.500 0.00 0.00 0.00 3.60
48 49 5.092781 CGCATTTATTCAAGCCTAAAACGT 58.907 37.500 0.00 0.00 0.00 3.99
49 50 6.092396 TCGCATTTATTCAAGCCTAAAACGTA 59.908 34.615 0.00 0.00 0.00 3.57
50 51 6.743627 CGCATTTATTCAAGCCTAAAACGTAA 59.256 34.615 0.00 0.00 0.00 3.18
51 52 7.431084 CGCATTTATTCAAGCCTAAAACGTAAT 59.569 33.333 0.00 0.00 0.00 1.89
52 53 9.083080 GCATTTATTCAAGCCTAAAACGTAATT 57.917 29.630 0.00 0.00 0.00 1.40
63 64 9.281075 AGCCTAAAACGTAATTATTTTAAAGCG 57.719 29.630 13.64 4.44 36.11 4.68
64 65 8.046132 GCCTAAAACGTAATTATTTTAAAGCGC 58.954 33.333 0.00 0.00 31.63 5.92
65 66 8.525876 CCTAAAACGTAATTATTTTAAAGCGCC 58.474 33.333 2.29 0.00 31.63 6.53
66 67 9.281075 CTAAAACGTAATTATTTTAAAGCGCCT 57.719 29.630 2.29 0.00 31.63 5.52
68 69 9.791820 AAAACGTAATTATTTTAAAGCGCCTAT 57.208 25.926 2.29 0.00 0.00 2.57
69 70 9.791820 AAACGTAATTATTTTAAAGCGCCTATT 57.208 25.926 2.29 0.00 0.00 1.73
70 71 9.791820 AACGTAATTATTTTAAAGCGCCTATTT 57.208 25.926 2.29 0.06 0.00 1.40
75 76 4.987408 TTTTAAAGCGCCTATTTACCCC 57.013 40.909 2.29 0.00 0.00 4.95
76 77 2.643995 TAAAGCGCCTATTTACCCCC 57.356 50.000 2.29 0.00 0.00 5.40
92 93 1.839894 CCCCCTCTAGGCAACATCC 59.160 63.158 0.00 0.00 41.41 3.51
93 94 0.988145 CCCCCTCTAGGCAACATCCA 60.988 60.000 0.00 0.00 41.41 3.41
94 95 0.181350 CCCCTCTAGGCAACATCCAC 59.819 60.000 0.00 0.00 41.41 4.02
95 96 0.179073 CCCTCTAGGCAACATCCACG 60.179 60.000 0.00 0.00 41.41 4.94
96 97 0.824109 CCTCTAGGCAACATCCACGA 59.176 55.000 0.00 0.00 41.41 4.35
97 98 1.414181 CCTCTAGGCAACATCCACGAT 59.586 52.381 0.00 0.00 41.41 3.73
98 99 2.546795 CCTCTAGGCAACATCCACGATC 60.547 54.545 0.00 0.00 41.41 3.69
99 100 2.363680 CTCTAGGCAACATCCACGATCT 59.636 50.000 0.00 0.00 41.41 2.75
100 101 2.766263 TCTAGGCAACATCCACGATCTT 59.234 45.455 0.00 0.00 41.41 2.40
101 102 2.496899 AGGCAACATCCACGATCTTT 57.503 45.000 0.00 0.00 41.41 2.52
102 103 3.627395 AGGCAACATCCACGATCTTTA 57.373 42.857 0.00 0.00 41.41 1.85
103 104 3.950397 AGGCAACATCCACGATCTTTAA 58.050 40.909 0.00 0.00 41.41 1.52
104 105 3.689649 AGGCAACATCCACGATCTTTAAC 59.310 43.478 0.00 0.00 41.41 2.01
105 106 3.485216 GGCAACATCCACGATCTTTAACG 60.485 47.826 0.00 0.00 0.00 3.18
106 107 3.124636 GCAACATCCACGATCTTTAACGT 59.875 43.478 0.00 0.00 43.50 3.99
107 108 4.378046 GCAACATCCACGATCTTTAACGTT 60.378 41.667 5.88 5.88 40.76 3.99
122 123 8.623310 TCTTTAACGTTTCTTCCATGAAAAAC 57.377 30.769 5.91 0.00 37.63 2.43
133 134 5.885449 TCCATGAAAAACCTCACCAAAAT 57.115 34.783 0.00 0.00 0.00 1.82
159 160 9.420551 TCTAAAAACTAAACAAAAGCCGAAAAA 57.579 25.926 0.00 0.00 0.00 1.94
161 162 8.888332 AAAAACTAAACAAAAGCCGAAAAATG 57.112 26.923 0.00 0.00 0.00 2.32
165 166 8.705048 ACTAAACAAAAGCCGAAAAATGTAAA 57.295 26.923 0.00 0.00 0.00 2.01
166 167 9.152595 ACTAAACAAAAGCCGAAAAATGTAAAA 57.847 25.926 0.00 0.00 0.00 1.52
167 168 9.974750 CTAAACAAAAGCCGAAAAATGTAAAAA 57.025 25.926 0.00 0.00 0.00 1.94
218 219 6.509418 TTTTTGAAATCCCGAGGATACAAG 57.491 37.500 16.49 0.00 42.27 3.16
219 220 3.194005 TGAAATCCCGAGGATACAAGC 57.806 47.619 5.94 0.00 42.27 4.01
225 226 1.519234 CGAGGATACAAGCAGCGCA 60.519 57.895 11.47 0.00 41.41 6.09
227 228 1.756375 GAGGATACAAGCAGCGCACG 61.756 60.000 11.47 0.01 41.41 5.34
238 239 1.594021 AGCGCACGACACATGACAA 60.594 52.632 11.47 0.00 0.00 3.18
267 268 1.939934 CTCACAAAGGACGTGCTTTCA 59.060 47.619 29.28 16.28 34.27 2.69
269 270 2.096819 TCACAAAGGACGTGCTTTCAAC 59.903 45.455 29.28 0.00 34.27 3.18
270 271 1.404035 ACAAAGGACGTGCTTTCAACC 59.596 47.619 29.28 4.75 0.00 3.77
272 273 0.106918 AAGGACGTGCTTTCAACCCA 60.107 50.000 17.37 0.00 0.00 4.51
273 274 0.110486 AGGACGTGCTTTCAACCCAT 59.890 50.000 2.68 0.00 0.00 4.00
274 275 0.958822 GGACGTGCTTTCAACCCATT 59.041 50.000 0.00 0.00 0.00 3.16
275 276 2.156098 GGACGTGCTTTCAACCCATTA 58.844 47.619 0.00 0.00 0.00 1.90
276 277 2.554893 GGACGTGCTTTCAACCCATTAA 59.445 45.455 0.00 0.00 0.00 1.40
280 281 5.606505 ACGTGCTTTCAACCCATTAAAAAT 58.393 33.333 0.00 0.00 0.00 1.82
281 282 5.465056 ACGTGCTTTCAACCCATTAAAAATG 59.535 36.000 0.00 0.00 0.00 2.32
283 284 4.759183 TGCTTTCAACCCATTAAAAATGCC 59.241 37.500 0.00 0.00 0.00 4.40
284 285 4.142924 GCTTTCAACCCATTAAAAATGCCG 60.143 41.667 0.00 0.00 0.00 5.69
285 286 2.966050 TCAACCCATTAAAAATGCCGC 58.034 42.857 0.00 0.00 0.00 6.53
286 287 2.564947 TCAACCCATTAAAAATGCCGCT 59.435 40.909 0.00 0.00 0.00 5.52
287 288 3.764434 TCAACCCATTAAAAATGCCGCTA 59.236 39.130 0.00 0.00 0.00 4.26
288 289 4.111916 CAACCCATTAAAAATGCCGCTAG 58.888 43.478 0.00 0.00 0.00 3.42
290 291 3.767131 ACCCATTAAAAATGCCGCTAGTT 59.233 39.130 0.00 0.00 0.00 2.24
293 294 4.359706 CATTAAAAATGCCGCTAGTTCCC 58.640 43.478 0.00 0.00 0.00 3.97
294 295 2.215942 AAAAATGCCGCTAGTTCCCT 57.784 45.000 0.00 0.00 0.00 4.20
327 328 9.833917 GGCACTCTCTAATTAGTATTTTTAGGT 57.166 33.333 12.19 0.00 0.00 3.08
389 390 1.094785 AGTTGGTTCCATATGCGTGC 58.905 50.000 0.00 0.00 0.00 5.34
390 391 0.100503 GTTGGTTCCATATGCGTGCC 59.899 55.000 0.00 0.00 0.00 5.01
392 393 2.542907 GGTTCCATATGCGTGCCGG 61.543 63.158 0.00 0.00 0.00 6.13
429 464 3.657350 GTTGGTGCAGGGGCCCTA 61.657 66.667 28.28 8.18 40.13 3.53
462 497 2.203437 AGGTTTGGTTGACCGCCC 60.203 61.111 0.00 0.00 42.11 6.13
464 499 2.903350 GTTTGGTTGACCGCCCGT 60.903 61.111 0.00 0.00 39.43 5.28
465 500 2.902846 TTTGGTTGACCGCCCGTG 60.903 61.111 0.00 0.00 39.43 4.94
484 1145 3.842923 CGCCGTGAGAGATGCCCT 61.843 66.667 0.00 0.00 0.00 5.19
487 1148 2.801631 CCGTGAGAGATGCCCTCCC 61.802 68.421 0.20 0.00 42.97 4.30
527 1200 2.672098 AGTGCATACTCCCTAGACCTG 58.328 52.381 0.00 0.00 28.79 4.00
530 1203 4.106502 AGTGCATACTCCCTAGACCTGATA 59.893 45.833 0.00 0.00 28.79 2.15
537 1210 4.173043 ACTCCCTAGACCTGATAATTCCCT 59.827 45.833 0.00 0.00 0.00 4.20
540 1213 4.493618 CCTAGACCTGATAATTCCCTGGA 58.506 47.826 0.00 0.00 0.00 3.86
541 1214 4.284746 CCTAGACCTGATAATTCCCTGGAC 59.715 50.000 0.00 4.46 0.00 4.02
543 1216 1.768870 ACCTGATAATTCCCTGGACCG 59.231 52.381 0.00 0.00 0.00 4.79
604 1294 1.503542 GCCCGAAGCACATGAACAG 59.496 57.895 0.00 0.00 42.97 3.16
605 1295 1.237285 GCCCGAAGCACATGAACAGT 61.237 55.000 0.00 0.00 42.97 3.55
609 1299 1.002576 CGAAGCACATGAACAGTTGCA 60.003 47.619 0.00 0.00 0.00 4.08
694 1389 9.851686 CAGATATATATAGGCATTTTGGGCTTA 57.148 33.333 0.00 0.00 44.09 3.09
700 1395 3.954200 AGGCATTTTGGGCTTATTTTGG 58.046 40.909 0.00 0.00 41.46 3.28
701 1396 3.016031 GGCATTTTGGGCTTATTTTGGG 58.984 45.455 0.00 0.00 0.00 4.12
702 1397 2.423185 GCATTTTGGGCTTATTTTGGGC 59.577 45.455 0.00 0.00 0.00 5.36
703 1398 3.873410 GCATTTTGGGCTTATTTTGGGCT 60.873 43.478 0.00 0.00 0.00 5.19
704 1399 4.334552 CATTTTGGGCTTATTTTGGGCTT 58.665 39.130 0.00 0.00 0.00 4.35
719 1414 3.747976 CTTTTGGGCCGGGCTTCG 61.748 66.667 28.80 8.36 38.88 3.79
734 1429 2.159382 GCTTCGGGTGAGAAATTGGAA 58.841 47.619 0.00 0.00 0.00 3.53
738 1433 1.173913 GGGTGAGAAATTGGAACCCG 58.826 55.000 3.81 0.00 41.08 5.28
762 1458 3.880846 GCCGAATGCTGGGCTTCG 61.881 66.667 13.05 13.05 45.93 3.79
823 1519 0.478942 TACTCCCCCTCCTCTCATCG 59.521 60.000 0.00 0.00 0.00 3.84
911 1616 1.460504 AGTCGGTAGATTGACTCGCA 58.539 50.000 0.00 0.00 41.46 5.10
923 1628 1.268743 TGACTCGCATGTGCTAGATCG 60.269 52.381 12.72 0.00 37.30 3.69
934 1639 3.256716 CTAGATCGAGGCCGCGTCC 62.257 68.421 28.27 19.80 35.37 4.79
990 1698 2.203549 AAAGGGTAGAGCAGCAGGGC 62.204 60.000 0.00 0.00 0.00 5.19
991 1699 3.402681 GGGTAGAGCAGCAGGGCA 61.403 66.667 0.00 0.00 35.83 5.36
992 1700 2.188994 GGTAGAGCAGCAGGGCAG 59.811 66.667 0.00 0.00 35.83 4.85
993 1701 2.362369 GGTAGAGCAGCAGGGCAGA 61.362 63.158 0.00 0.00 35.83 4.26
1008 1719 1.410153 GGCAGATCGGCAATGGAAAAT 59.590 47.619 19.63 0.00 40.76 1.82
1062 1773 3.971702 GGCCCAGCCTTGTGGACT 61.972 66.667 0.00 0.00 46.69 3.85
1505 2222 6.127338 ACTGAAGAATGTCCATCGATTGAGTA 60.127 38.462 0.00 0.00 0.00 2.59
1528 2245 3.485431 CTCTGCTTGCAGCCGTCG 61.485 66.667 16.91 0.00 41.51 5.12
1552 2269 7.703197 TCGCTGTTTTATGTTCGTCTGAATATA 59.297 33.333 0.00 0.00 37.20 0.86
1685 2415 2.800544 GCGCCTCACATATACACGAATT 59.199 45.455 0.00 0.00 0.00 2.17
1718 2448 8.696410 TTGATTGGTTGAGTTTACAAAGTTTC 57.304 30.769 0.00 0.00 0.00 2.78
1730 2460 9.952188 AGTTTACAAAGTTTCTTATTCTTCTGC 57.048 29.630 0.00 0.00 0.00 4.26
1789 2532 5.344743 TCTGGAACAATCATCTGACTACC 57.655 43.478 0.00 0.00 38.70 3.18
1790 2533 5.026121 TCTGGAACAATCATCTGACTACCT 58.974 41.667 0.00 0.00 38.70 3.08
1791 2534 6.194967 TCTGGAACAATCATCTGACTACCTA 58.805 40.000 0.00 0.00 38.70 3.08
1792 2535 6.322456 TCTGGAACAATCATCTGACTACCTAG 59.678 42.308 0.00 0.00 38.70 3.02
1793 2536 6.194967 TGGAACAATCATCTGACTACCTAGA 58.805 40.000 0.00 0.00 31.92 2.43
1794 2537 6.322456 TGGAACAATCATCTGACTACCTAGAG 59.678 42.308 0.00 0.00 31.92 2.43
1795 2538 6.239176 GGAACAATCATCTGACTACCTAGAGG 60.239 46.154 0.00 0.00 42.17 3.69
1796 2539 6.019656 ACAATCATCTGACTACCTAGAGGA 57.980 41.667 1.60 0.00 38.01 3.71
1797 2540 6.068010 ACAATCATCTGACTACCTAGAGGAG 58.932 44.000 1.60 0.00 37.19 3.69
1798 2541 5.922960 ATCATCTGACTACCTAGAGGAGT 57.077 43.478 1.60 1.65 37.19 3.85
1799 2542 5.718801 TCATCTGACTACCTAGAGGAGTT 57.281 43.478 1.60 0.00 38.94 3.01
1800 2543 6.080969 TCATCTGACTACCTAGAGGAGTTT 57.919 41.667 1.60 0.00 38.94 2.66
1801 2544 7.209340 TCATCTGACTACCTAGAGGAGTTTA 57.791 40.000 1.60 0.00 38.94 2.01
1802 2545 7.817440 TCATCTGACTACCTAGAGGAGTTTAT 58.183 38.462 1.60 0.00 38.94 1.40
1803 2546 7.940137 TCATCTGACTACCTAGAGGAGTTTATC 59.060 40.741 1.60 0.00 38.94 1.75
1804 2547 7.454553 TCTGACTACCTAGAGGAGTTTATCT 57.545 40.000 1.60 0.00 38.94 1.98
1805 2548 7.284074 TCTGACTACCTAGAGGAGTTTATCTG 58.716 42.308 1.60 0.00 38.94 2.90
1806 2549 7.127493 TCTGACTACCTAGAGGAGTTTATCTGA 59.873 40.741 1.60 0.00 38.94 3.27
1807 2550 7.055378 TGACTACCTAGAGGAGTTTATCTGAC 58.945 42.308 1.60 0.00 38.94 3.51
1808 2551 7.092354 TGACTACCTAGAGGAGTTTATCTGACT 60.092 40.741 1.60 0.00 38.94 3.41
1809 2552 8.334522 ACTACCTAGAGGAGTTTATCTGACTA 57.665 38.462 1.60 0.00 38.94 2.59
1810 2553 8.212995 ACTACCTAGAGGAGTTTATCTGACTAC 58.787 40.741 1.60 0.00 38.94 2.73
1811 2554 6.367161 ACCTAGAGGAGTTTATCTGACTACC 58.633 44.000 1.60 0.00 38.94 3.18
1812 2555 6.160814 ACCTAGAGGAGTTTATCTGACTACCT 59.839 42.308 1.60 0.00 38.94 3.08
1813 2556 7.350389 ACCTAGAGGAGTTTATCTGACTACCTA 59.650 40.741 1.60 0.00 38.94 3.08
1814 2557 7.881232 CCTAGAGGAGTTTATCTGACTACCTAG 59.119 44.444 0.00 0.00 37.39 3.02
1815 2558 7.454553 AGAGGAGTTTATCTGACTACCTAGA 57.545 40.000 0.00 0.00 30.21 2.43
1816 2559 7.514721 AGAGGAGTTTATCTGACTACCTAGAG 58.485 42.308 0.00 0.00 30.21 2.43
1817 2560 6.607019 AGGAGTTTATCTGACTACCTAGAGG 58.393 44.000 0.00 0.00 42.17 3.69
1818 2561 6.390461 AGGAGTTTATCTGACTACCTAGAGGA 59.610 42.308 1.60 0.00 38.94 3.71
1819 2562 6.713450 GGAGTTTATCTGACTACCTAGAGGAG 59.287 46.154 1.60 0.00 38.94 3.69
1820 2563 7.215743 AGTTTATCTGACTACCTAGAGGAGT 57.784 40.000 1.60 1.65 38.94 3.85
1821 2564 7.645002 AGTTTATCTGACTACCTAGAGGAGTT 58.355 38.462 1.60 0.00 38.94 3.01
1822 2565 8.117312 AGTTTATCTGACTACCTAGAGGAGTTT 58.883 37.037 1.60 0.00 38.94 2.66
1829 2572 7.055378 TGACTACCTAGAGGAGTTTATCTGAC 58.945 42.308 1.60 0.00 38.94 3.51
1845 2588 7.883391 TTATCTGACTACCTAGAGGAGTTTG 57.117 40.000 1.60 0.45 38.94 2.93
1853 2596 3.244981 ACCTAGAGGAGTTTGTCGAGTCT 60.245 47.826 1.60 0.00 38.94 3.24
1865 2608 2.362369 CGAGTCTGGGGCTGGACAT 61.362 63.158 0.00 0.00 35.18 3.06
1866 2609 1.222936 GAGTCTGGGGCTGGACATG 59.777 63.158 0.00 0.00 35.18 3.21
1868 2611 1.078143 GTCTGGGGCTGGACATGTC 60.078 63.158 17.91 17.91 33.19 3.06
1900 3225 2.805164 TGGAAGGCCAGGATTCCTT 58.195 52.632 19.27 10.22 44.46 3.36
1904 3229 3.272020 TGGAAGGCCAGGATTCCTTTTAT 59.728 43.478 19.27 0.00 44.46 1.40
1915 3770 7.922811 CCAGGATTCCTTTTATGATTAAAGTGC 59.077 37.037 1.28 0.00 32.06 4.40
1922 3777 9.616156 TCCTTTTATGATTAAAGTGCGGTTATA 57.384 29.630 3.62 0.00 32.06 0.98
1930 3785 7.602644 TGATTAAAGTGCGGTTATATCTGATCC 59.397 37.037 0.00 0.00 0.00 3.36
1940 3795 1.882912 TATCTGATCCGGCACAATGC 58.117 50.000 0.00 0.00 44.08 3.56
1950 3805 2.948093 GCACAATGCCATTGCTACG 58.052 52.632 17.14 5.05 43.98 3.51
1969 3824 9.997482 TTGCTACGAAAGATAATATGGAAAAAC 57.003 29.630 0.00 0.00 0.00 2.43
1973 3828 7.186804 ACGAAAGATAATATGGAAAAACGCAG 58.813 34.615 0.00 0.00 0.00 5.18
1975 3830 8.070171 CGAAAGATAATATGGAAAAACGCAGAT 58.930 33.333 0.00 0.00 0.00 2.90
1977 3832 7.206981 AGATAATATGGAAAAACGCAGATGG 57.793 36.000 0.00 0.00 0.00 3.51
2014 3869 7.167968 ACACTTGTCGATTTTGTGATGAAAATG 59.832 33.333 14.48 0.00 36.00 2.32
2039 5997 9.060347 TGAGAGCATCCATCATTTATTCTTTAC 57.940 33.333 0.00 0.00 33.66 2.01
2057 6015 4.981806 TTACTTGTTCTGCTGCTGTTTT 57.018 36.364 0.00 0.00 0.00 2.43
2070 6028 4.731773 GCTGCTGTTTTATATGTGGAGCAC 60.732 45.833 0.00 0.00 38.44 4.40
2071 6029 3.694072 TGCTGTTTTATATGTGGAGCACC 59.306 43.478 0.00 0.00 32.73 5.01
2139 6109 6.092259 ACACAATACTTAGCGAAGAACATTCC 59.908 38.462 13.94 0.00 36.45 3.01
2143 6113 3.432252 ACTTAGCGAAGAACATTCCGTTG 59.568 43.478 13.94 0.00 38.19 4.10
2148 6118 0.112412 AAGAACATTCCGTTGGGCCT 59.888 50.000 4.53 0.00 38.19 5.19
2154 6124 2.167662 CATTCCGTTGGGCCTTAACTT 58.832 47.619 17.32 2.34 0.00 2.66
2162 6132 3.237268 TGGGCCTTAACTTTCATGTGT 57.763 42.857 4.53 0.00 0.00 3.72
2163 6133 2.890311 TGGGCCTTAACTTTCATGTGTG 59.110 45.455 4.53 0.00 0.00 3.82
2166 6136 2.352715 GCCTTAACTTTCATGTGTGGGC 60.353 50.000 0.00 0.00 0.00 5.36
2167 6137 2.890311 CCTTAACTTTCATGTGTGGGCA 59.110 45.455 0.00 0.00 0.00 5.36
2168 6138 3.511146 CCTTAACTTTCATGTGTGGGCAT 59.489 43.478 0.00 0.00 0.00 4.40
2169 6139 4.021192 CCTTAACTTTCATGTGTGGGCATT 60.021 41.667 0.00 0.00 0.00 3.56
2170 6140 3.389925 AACTTTCATGTGTGGGCATTG 57.610 42.857 0.00 0.00 0.00 2.82
2171 6141 1.001181 ACTTTCATGTGTGGGCATTGC 59.999 47.619 0.00 0.00 0.00 3.56
2172 6142 1.001068 CTTTCATGTGTGGGCATTGCA 59.999 47.619 11.39 0.00 0.00 4.08
2173 6143 0.604073 TTCATGTGTGGGCATTGCAG 59.396 50.000 11.39 0.00 0.00 4.41
2174 6144 1.447140 CATGTGTGGGCATTGCAGC 60.447 57.895 11.39 0.35 0.00 5.25
2193 6163 0.104671 CCTTTTGCTGGGTGTTGTGG 59.895 55.000 0.00 0.00 0.00 4.17
2212 6182 4.222145 TGTGGAAAACTCGTAATAGAGCCT 59.778 41.667 0.00 0.00 41.77 4.58
2213 6183 4.567159 GTGGAAAACTCGTAATAGAGCCTG 59.433 45.833 0.00 0.00 41.77 4.85
2214 6184 3.556365 GGAAAACTCGTAATAGAGCCTGC 59.444 47.826 0.00 0.00 41.77 4.85
2215 6185 4.434520 GAAAACTCGTAATAGAGCCTGCT 58.565 43.478 0.00 0.00 41.77 4.24
2224 6194 7.217200 TCGTAATAGAGCCTGCTTTTGATAAT 58.783 34.615 0.00 0.00 0.00 1.28
2225 6195 8.364894 TCGTAATAGAGCCTGCTTTTGATAATA 58.635 33.333 0.00 0.00 0.00 0.98
2256 6226 1.606531 AGCCCCTGTTGAGCTGATC 59.393 57.895 0.00 0.00 34.99 2.92
2266 6236 3.686241 TGTTGAGCTGATCTGTTACATGC 59.314 43.478 0.00 0.00 0.00 4.06
2268 6238 2.166254 TGAGCTGATCTGTTACATGCGA 59.834 45.455 0.00 0.00 0.00 5.10
2269 6239 3.181472 TGAGCTGATCTGTTACATGCGAT 60.181 43.478 0.00 0.00 0.00 4.58
2287 6257 3.064207 CGATCTTTCCTTCGTGTTTGGA 58.936 45.455 0.00 0.00 0.00 3.53
2353 6323 0.445436 GGCGAGTCTGCAACAGATTG 59.555 55.000 0.00 0.00 42.73 2.67
2380 6350 1.153686 GCTCATGAGACTGCGCAGA 60.154 57.895 42.03 21.72 0.00 4.26
2434 6404 1.131420 GCTGAAGCTGAAGTTCGCG 59.869 57.895 0.00 0.00 38.21 5.87
2443 6415 0.606096 TGAAGTTCGCGGATCTGGAA 59.394 50.000 6.13 2.70 0.00 3.53
2449 6421 0.174845 TCGCGGATCTGGAAAACGAT 59.825 50.000 6.13 0.00 0.00 3.73
2468 6440 1.637338 TGAGATGCTGGAGTGACTGT 58.363 50.000 0.00 0.00 0.00 3.55
2469 6441 1.274447 TGAGATGCTGGAGTGACTGTG 59.726 52.381 0.00 0.00 0.00 3.66
2473 6445 0.541392 TGCTGGAGTGACTGTGTTGT 59.459 50.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.963383 AATGCGAAATAAACCTAGCGG 57.037 42.857 0.00 0.00 0.00 5.52
11 12 7.129622 TGAATAAATGCGAAATAAACCTAGCG 58.870 34.615 0.00 0.00 0.00 4.26
12 13 8.850454 TTGAATAAATGCGAAATAAACCTAGC 57.150 30.769 0.00 0.00 0.00 3.42
13 14 8.958043 GCTTGAATAAATGCGAAATAAACCTAG 58.042 33.333 0.00 0.00 0.00 3.02
14 15 7.918562 GGCTTGAATAAATGCGAAATAAACCTA 59.081 33.333 0.00 0.00 0.00 3.08
15 16 6.756542 GGCTTGAATAAATGCGAAATAAACCT 59.243 34.615 0.00 0.00 0.00 3.50
16 17 6.756542 AGGCTTGAATAAATGCGAAATAAACC 59.243 34.615 0.00 0.00 0.00 3.27
17 18 7.755582 AGGCTTGAATAAATGCGAAATAAAC 57.244 32.000 0.00 0.00 0.00 2.01
18 19 9.862371 TTTAGGCTTGAATAAATGCGAAATAAA 57.138 25.926 0.00 0.00 0.00 1.40
19 20 9.862371 TTTTAGGCTTGAATAAATGCGAAATAA 57.138 25.926 0.00 0.00 0.00 1.40
20 21 9.296400 GTTTTAGGCTTGAATAAATGCGAAATA 57.704 29.630 0.00 0.00 0.00 1.40
21 22 7.009174 CGTTTTAGGCTTGAATAAATGCGAAAT 59.991 33.333 0.00 0.00 0.00 2.17
22 23 6.306837 CGTTTTAGGCTTGAATAAATGCGAAA 59.693 34.615 0.00 0.00 0.00 3.46
23 24 5.797934 CGTTTTAGGCTTGAATAAATGCGAA 59.202 36.000 0.00 0.00 0.00 4.70
24 25 5.106475 ACGTTTTAGGCTTGAATAAATGCGA 60.106 36.000 0.00 0.00 0.00 5.10
25 26 5.092781 ACGTTTTAGGCTTGAATAAATGCG 58.907 37.500 0.00 0.00 0.00 4.73
26 27 8.628882 ATTACGTTTTAGGCTTGAATAAATGC 57.371 30.769 0.00 0.00 0.00 3.56
37 38 9.281075 CGCTTTAAAATAATTACGTTTTAGGCT 57.719 29.630 17.36 0.00 33.02 4.58
38 39 8.046132 GCGCTTTAAAATAATTACGTTTTAGGC 58.954 33.333 0.00 13.84 33.02 3.93
39 40 8.525876 GGCGCTTTAAAATAATTACGTTTTAGG 58.474 33.333 7.64 3.36 33.02 2.69
40 41 9.281075 AGGCGCTTTAAAATAATTACGTTTTAG 57.719 29.630 7.64 2.92 33.02 1.85
42 43 9.791820 ATAGGCGCTTTAAAATAATTACGTTTT 57.208 25.926 7.64 3.10 0.00 2.43
43 44 9.791820 AATAGGCGCTTTAAAATAATTACGTTT 57.208 25.926 7.64 0.00 0.00 3.60
44 45 9.791820 AAATAGGCGCTTTAAAATAATTACGTT 57.208 25.926 7.64 0.00 0.00 3.99
49 50 8.145767 GGGGTAAATAGGCGCTTTAAAATAATT 58.854 33.333 7.64 0.00 0.00 1.40
50 51 7.256048 GGGGGTAAATAGGCGCTTTAAAATAAT 60.256 37.037 7.64 0.00 0.00 1.28
51 52 6.040729 GGGGGTAAATAGGCGCTTTAAAATAA 59.959 38.462 7.64 0.00 0.00 1.40
52 53 5.535783 GGGGGTAAATAGGCGCTTTAAAATA 59.464 40.000 7.64 0.00 0.00 1.40
53 54 4.342951 GGGGGTAAATAGGCGCTTTAAAAT 59.657 41.667 7.64 0.00 0.00 1.82
54 55 3.700539 GGGGGTAAATAGGCGCTTTAAAA 59.299 43.478 7.64 0.00 0.00 1.52
55 56 3.289836 GGGGGTAAATAGGCGCTTTAAA 58.710 45.455 7.64 0.00 0.00 1.52
56 57 2.934887 GGGGGTAAATAGGCGCTTTAA 58.065 47.619 7.64 0.00 0.00 1.52
57 58 2.643995 GGGGGTAAATAGGCGCTTTA 57.356 50.000 7.64 1.20 0.00 1.85
58 59 3.507675 GGGGGTAAATAGGCGCTTT 57.492 52.632 7.64 2.35 0.00 3.51
74 75 0.988145 TGGATGTTGCCTAGAGGGGG 60.988 60.000 0.00 0.00 35.18 5.40
75 76 0.181350 GTGGATGTTGCCTAGAGGGG 59.819 60.000 0.00 0.00 35.18 4.79
76 77 0.179073 CGTGGATGTTGCCTAGAGGG 60.179 60.000 0.00 0.00 35.18 4.30
77 78 0.824109 TCGTGGATGTTGCCTAGAGG 59.176 55.000 0.00 0.00 38.53 3.69
78 79 2.363680 AGATCGTGGATGTTGCCTAGAG 59.636 50.000 0.00 0.00 0.00 2.43
79 80 2.388735 AGATCGTGGATGTTGCCTAGA 58.611 47.619 0.00 0.00 0.00 2.43
80 81 2.898729 AGATCGTGGATGTTGCCTAG 57.101 50.000 0.00 0.00 0.00 3.02
81 82 3.627395 AAAGATCGTGGATGTTGCCTA 57.373 42.857 0.00 0.00 0.00 3.93
82 83 2.496899 AAAGATCGTGGATGTTGCCT 57.503 45.000 0.00 0.00 0.00 4.75
83 84 3.485216 CGTTAAAGATCGTGGATGTTGCC 60.485 47.826 0.00 0.00 0.00 4.52
84 85 3.124636 ACGTTAAAGATCGTGGATGTTGC 59.875 43.478 0.00 0.00 38.85 4.17
85 86 4.921470 ACGTTAAAGATCGTGGATGTTG 57.079 40.909 0.00 0.00 38.85 3.33
86 87 5.699458 AGAAACGTTAAAGATCGTGGATGTT 59.301 36.000 0.00 0.00 40.19 2.71
87 88 5.235516 AGAAACGTTAAAGATCGTGGATGT 58.764 37.500 0.00 0.00 40.19 3.06
88 89 5.779806 AGAAACGTTAAAGATCGTGGATG 57.220 39.130 0.00 0.00 40.19 3.51
89 90 5.350640 GGAAGAAACGTTAAAGATCGTGGAT 59.649 40.000 0.00 0.00 40.19 3.41
90 91 4.687483 GGAAGAAACGTTAAAGATCGTGGA 59.313 41.667 0.00 0.00 40.19 4.02
91 92 4.449743 TGGAAGAAACGTTAAAGATCGTGG 59.550 41.667 0.00 0.00 40.19 4.94
92 93 5.585500 TGGAAGAAACGTTAAAGATCGTG 57.415 39.130 0.00 0.00 40.19 4.35
93 94 5.929992 TCATGGAAGAAACGTTAAAGATCGT 59.070 36.000 0.00 0.00 42.12 3.73
94 95 6.403333 TCATGGAAGAAACGTTAAAGATCG 57.597 37.500 0.00 0.00 0.00 3.69
95 96 9.458374 TTTTTCATGGAAGAAACGTTAAAGATC 57.542 29.630 0.00 0.00 37.24 2.75
96 97 9.244799 GTTTTTCATGGAAGAAACGTTAAAGAT 57.755 29.630 0.00 0.00 37.24 2.40
97 98 7.703197 GGTTTTTCATGGAAGAAACGTTAAAGA 59.297 33.333 0.00 0.00 37.24 2.52
98 99 7.704899 AGGTTTTTCATGGAAGAAACGTTAAAG 59.295 33.333 0.00 0.00 37.24 1.85
99 100 7.548967 AGGTTTTTCATGGAAGAAACGTTAAA 58.451 30.769 0.00 0.00 37.24 1.52
100 101 7.102847 AGGTTTTTCATGGAAGAAACGTTAA 57.897 32.000 0.00 0.00 37.24 2.01
101 102 6.319152 TGAGGTTTTTCATGGAAGAAACGTTA 59.681 34.615 0.00 0.00 37.24 3.18
102 103 5.126384 TGAGGTTTTTCATGGAAGAAACGTT 59.874 36.000 0.00 0.00 37.24 3.99
103 104 4.642885 TGAGGTTTTTCATGGAAGAAACGT 59.357 37.500 0.00 0.00 37.24 3.99
104 105 4.976116 GTGAGGTTTTTCATGGAAGAAACG 59.024 41.667 0.00 0.00 37.24 3.60
105 106 5.163457 TGGTGAGGTTTTTCATGGAAGAAAC 60.163 40.000 0.00 0.00 37.24 2.78
106 107 4.959210 TGGTGAGGTTTTTCATGGAAGAAA 59.041 37.500 0.00 0.00 35.82 2.52
107 108 4.541705 TGGTGAGGTTTTTCATGGAAGAA 58.458 39.130 0.00 0.00 0.00 2.52
122 123 9.810545 TTGTTTAGTTTTTAGATTTTGGTGAGG 57.189 29.630 0.00 0.00 0.00 3.86
133 134 8.983307 TTTTCGGCTTTTGTTTAGTTTTTAGA 57.017 26.923 0.00 0.00 0.00 2.10
199 200 2.503765 TGCTTGTATCCTCGGGATTTCA 59.496 45.455 10.21 8.03 39.79 2.69
200 201 3.134458 CTGCTTGTATCCTCGGGATTTC 58.866 50.000 10.21 6.02 39.79 2.17
203 204 0.394565 GCTGCTTGTATCCTCGGGAT 59.605 55.000 9.89 9.89 45.40 3.85
204 205 1.823295 GCTGCTTGTATCCTCGGGA 59.177 57.895 0.00 0.00 35.55 5.14
207 208 1.519234 TGCGCTGCTTGTATCCTCG 60.519 57.895 9.73 0.00 0.00 4.63
209 210 1.811266 CGTGCGCTGCTTGTATCCT 60.811 57.895 9.73 0.00 0.00 3.24
212 213 1.374125 TGTCGTGCGCTGCTTGTAT 60.374 52.632 9.73 0.00 0.00 2.29
217 218 3.417224 CATGTGTCGTGCGCTGCT 61.417 61.111 9.73 0.00 0.00 4.24
218 219 3.413861 TCATGTGTCGTGCGCTGC 61.414 61.111 9.73 0.00 0.00 5.25
219 220 1.830368 TTGTCATGTGTCGTGCGCTG 61.830 55.000 9.73 0.40 0.00 5.18
225 226 3.111853 ACATCTGTTGTCATGTGTCGT 57.888 42.857 0.00 0.00 30.89 4.34
249 250 2.450160 GTTGAAAGCACGTCCTTTGTG 58.550 47.619 9.70 0.00 40.32 3.33
250 251 1.404035 GGTTGAAAGCACGTCCTTTGT 59.596 47.619 9.70 0.00 35.31 2.83
251 252 1.269051 GGGTTGAAAGCACGTCCTTTG 60.269 52.381 9.70 0.00 35.31 2.77
254 255 0.110486 ATGGGTTGAAAGCACGTCCT 59.890 50.000 0.00 0.00 0.00 3.85
255 256 0.958822 AATGGGTTGAAAGCACGTCC 59.041 50.000 0.00 0.00 0.00 4.79
258 259 5.614449 GCATTTTTAATGGGTTGAAAGCACG 60.614 40.000 1.99 0.00 0.00 5.34
260 261 4.759183 GGCATTTTTAATGGGTTGAAAGCA 59.241 37.500 1.99 0.00 0.00 3.91
261 262 4.142924 CGGCATTTTTAATGGGTTGAAAGC 60.143 41.667 1.99 0.00 0.00 3.51
267 268 3.767131 ACTAGCGGCATTTTTAATGGGTT 59.233 39.130 1.45 0.00 0.00 4.11
269 270 4.359706 GAACTAGCGGCATTTTTAATGGG 58.640 43.478 1.45 0.00 0.00 4.00
270 271 4.359706 GGAACTAGCGGCATTTTTAATGG 58.640 43.478 1.45 0.00 0.00 3.16
272 273 4.278310 AGGGAACTAGCGGCATTTTTAAT 58.722 39.130 1.45 0.00 40.61 1.40
273 274 3.692690 AGGGAACTAGCGGCATTTTTAA 58.307 40.909 1.45 0.00 40.61 1.52
274 275 3.359695 AGGGAACTAGCGGCATTTTTA 57.640 42.857 1.45 0.00 40.61 1.52
275 276 2.215942 AGGGAACTAGCGGCATTTTT 57.784 45.000 1.45 0.00 40.61 1.94
276 277 1.818674 CAAGGGAACTAGCGGCATTTT 59.181 47.619 1.45 0.00 42.68 1.82
280 281 0.902984 TCTCAAGGGAACTAGCGGCA 60.903 55.000 1.45 0.00 42.68 5.69
281 282 0.179097 CTCTCAAGGGAACTAGCGGC 60.179 60.000 0.00 0.00 42.68 6.53
355 356 6.492087 TGGAACCAACTAATTAGAGGGTTTTG 59.508 38.462 29.13 18.64 40.52 2.44
389 390 3.673484 CTGCCCTTGTTGTGCCGG 61.673 66.667 0.00 0.00 0.00 6.13
390 391 4.347453 GCTGCCCTTGTTGTGCCG 62.347 66.667 0.00 0.00 0.00 5.69
392 393 4.347453 CGGCTGCCCTTGTTGTGC 62.347 66.667 14.12 0.00 0.00 4.57
412 428 3.657350 TAGGGCCCCTGCACCAAC 61.657 66.667 21.43 0.00 44.14 3.77
464 499 4.819761 GCATCTCTCACGGCGGCA 62.820 66.667 13.24 0.00 0.00 5.69
466 501 4.899239 GGGCATCTCTCACGGCGG 62.899 72.222 13.24 0.00 0.00 6.13
467 502 3.781770 GAGGGCATCTCTCACGGCG 62.782 68.421 4.80 4.80 39.38 6.46
468 503 2.107953 GAGGGCATCTCTCACGGC 59.892 66.667 0.00 0.00 39.38 5.68
474 1135 0.329596 GTGTTTGGGAGGGCATCTCT 59.670 55.000 0.00 0.00 42.10 3.10
484 1145 0.466555 CCACGGAAAGGTGTTTGGGA 60.467 55.000 0.00 0.00 36.16 4.37
487 1148 0.673437 ATGCCACGGAAAGGTGTTTG 59.327 50.000 0.00 0.00 36.16 2.93
519 1192 4.284746 GGTCCAGGGAATTATCAGGTCTAG 59.715 50.000 0.00 0.00 0.00 2.43
537 1210 4.211330 TTTGCCAAGCCCGGTCCA 62.211 61.111 0.00 0.00 0.00 4.02
589 1279 1.002576 TGCAACTGTTCATGTGCTTCG 60.003 47.619 5.47 0.00 0.00 3.79
668 1358 8.757982 AAGCCCAAAATGCCTATATATATCTG 57.242 34.615 0.00 0.00 0.00 2.90
687 1382 2.039613 CCAAAAGCCCAAAATAAGCCCA 59.960 45.455 0.00 0.00 0.00 5.36
690 1385 2.083774 GCCCAAAAGCCCAAAATAAGC 58.916 47.619 0.00 0.00 0.00 3.09
701 1396 4.069232 GAAGCCCGGCCCAAAAGC 62.069 66.667 5.55 0.00 0.00 3.51
702 1397 3.747976 CGAAGCCCGGCCCAAAAG 61.748 66.667 5.55 0.00 33.91 2.27
712 1407 0.811281 CAATTTCTCACCCGAAGCCC 59.189 55.000 0.00 0.00 0.00 5.19
715 1410 2.488153 GGTTCCAATTTCTCACCCGAAG 59.512 50.000 0.00 0.00 0.00 3.79
719 1414 1.173913 CGGGTTCCAATTTCTCACCC 58.826 55.000 0.00 0.00 43.43 4.61
722 1417 1.613255 GGCTCGGGTTCCAATTTCTCA 60.613 52.381 0.00 0.00 0.00 3.27
753 1449 4.778143 CCCGAACCCGAAGCCCAG 62.778 72.222 0.00 0.00 38.22 4.45
784 1480 6.255887 GGAGTATTAAACCTGTTCATCGACAG 59.744 42.308 0.00 0.00 45.19 3.51
789 1485 5.104067 AGGGGGAGTATTAAACCTGTTCATC 60.104 44.000 0.00 0.00 0.00 2.92
866 1571 2.127869 TCCGGCTCCGATCAAGAGG 61.128 63.158 10.28 6.38 42.83 3.69
893 1598 2.120232 CATGCGAGTCAATCTACCGAC 58.880 52.381 0.00 0.00 0.00 4.79
911 1616 1.662608 CGGCCTCGATCTAGCACAT 59.337 57.895 0.00 0.00 39.00 3.21
934 1639 3.070018 AGACAATCAGCCTTTTGACGAG 58.930 45.455 0.00 0.00 0.00 4.18
937 1642 3.124297 CGAGAGACAATCAGCCTTTTGAC 59.876 47.826 0.00 0.00 0.00 3.18
990 1698 3.489738 GGTGATTTTCCATTGCCGATCTG 60.490 47.826 0.00 0.00 0.00 2.90
991 1699 2.689983 GGTGATTTTCCATTGCCGATCT 59.310 45.455 0.00 0.00 0.00 2.75
992 1700 2.426738 TGGTGATTTTCCATTGCCGATC 59.573 45.455 0.00 0.00 0.00 3.69
993 1701 2.166254 GTGGTGATTTTCCATTGCCGAT 59.834 45.455 0.00 0.00 37.30 4.18
1050 1761 2.154462 CGAATTTCAGTCCACAAGGCT 58.846 47.619 0.00 0.00 33.74 4.58
1237 1948 3.827898 CCTCGTCTCGCCCACCTC 61.828 72.222 0.00 0.00 0.00 3.85
1528 2245 9.586150 CATATATTCAGACGAACATAAAACAGC 57.414 33.333 0.00 0.00 32.81 4.40
1552 2269 2.693591 ACCACTCGTGATCGGTAATCAT 59.306 45.455 0.00 0.00 45.94 2.45
1567 2284 7.924103 AATTTCGAACAAAATTACACCACTC 57.076 32.000 0.00 0.00 37.14 3.51
1645 2366 1.529010 CAGGGCAAGCACCACTGAA 60.529 57.895 0.00 0.00 32.68 3.02
1666 2396 5.615544 GCATCAATTCGTGTATATGTGAGGC 60.616 44.000 0.00 0.00 34.71 4.70
1685 2415 6.839124 AAACTCAACCAATCAATAGCATCA 57.161 33.333 0.00 0.00 0.00 3.07
1718 2448 9.752274 GCGATATCAATTTAGCAGAAGAATAAG 57.248 33.333 3.12 0.00 0.00 1.73
1730 2460 7.369803 AGGCATTACAGCGATATCAATTTAG 57.630 36.000 3.12 0.00 34.64 1.85
1783 2526 7.284820 AGTCAGATAAACTCCTCTAGGTAGTC 58.715 42.308 0.00 0.00 36.34 2.59
1785 2528 7.662669 GGTAGTCAGATAAACTCCTCTAGGTAG 59.337 44.444 0.00 0.00 36.34 3.18
1786 2529 7.350389 AGGTAGTCAGATAAACTCCTCTAGGTA 59.650 40.741 0.00 0.00 36.34 3.08
1787 2530 6.160814 AGGTAGTCAGATAAACTCCTCTAGGT 59.839 42.308 0.00 0.00 36.34 3.08
1788 2531 6.607019 AGGTAGTCAGATAAACTCCTCTAGG 58.393 44.000 0.00 0.00 0.00 3.02
1789 2532 8.653191 TCTAGGTAGTCAGATAAACTCCTCTAG 58.347 40.741 0.00 0.00 31.28 2.43
1790 2533 8.564364 TCTAGGTAGTCAGATAAACTCCTCTA 57.436 38.462 0.00 0.00 31.28 2.43
1791 2534 7.420913 CCTCTAGGTAGTCAGATAAACTCCTCT 60.421 44.444 0.00 0.00 31.28 3.69
1792 2535 6.713450 CCTCTAGGTAGTCAGATAAACTCCTC 59.287 46.154 0.00 0.00 31.28 3.71
1793 2536 6.390461 TCCTCTAGGTAGTCAGATAAACTCCT 59.610 42.308 0.00 0.00 36.34 3.69
1794 2537 6.603224 TCCTCTAGGTAGTCAGATAAACTCC 58.397 44.000 0.00 0.00 36.34 3.85
1795 2538 7.284820 ACTCCTCTAGGTAGTCAGATAAACTC 58.715 42.308 0.00 0.00 36.34 3.01
1796 2539 7.215743 ACTCCTCTAGGTAGTCAGATAAACT 57.784 40.000 0.00 0.00 36.34 2.66
1797 2540 7.885009 AACTCCTCTAGGTAGTCAGATAAAC 57.115 40.000 0.00 0.00 36.34 2.01
1799 2542 9.796180 GATAAACTCCTCTAGGTAGTCAGATAA 57.204 37.037 0.00 0.00 36.34 1.75
1800 2543 9.173231 AGATAAACTCCTCTAGGTAGTCAGATA 57.827 37.037 0.00 0.00 36.34 1.98
1801 2544 7.942341 CAGATAAACTCCTCTAGGTAGTCAGAT 59.058 40.741 0.00 0.00 36.34 2.90
1802 2545 7.127493 TCAGATAAACTCCTCTAGGTAGTCAGA 59.873 40.741 0.00 0.00 36.34 3.27
1803 2546 7.227910 GTCAGATAAACTCCTCTAGGTAGTCAG 59.772 44.444 0.00 0.00 36.34 3.51
1804 2547 7.055378 GTCAGATAAACTCCTCTAGGTAGTCA 58.945 42.308 0.00 0.00 36.34 3.41
1805 2548 7.284820 AGTCAGATAAACTCCTCTAGGTAGTC 58.715 42.308 0.00 0.00 36.34 2.59
1806 2549 7.215743 AGTCAGATAAACTCCTCTAGGTAGT 57.784 40.000 0.00 0.00 36.34 2.73
1807 2550 7.662669 GGTAGTCAGATAAACTCCTCTAGGTAG 59.337 44.444 0.00 0.00 36.34 3.18
1808 2551 7.350389 AGGTAGTCAGATAAACTCCTCTAGGTA 59.650 40.741 0.00 0.00 36.34 3.08
1809 2552 6.160814 AGGTAGTCAGATAAACTCCTCTAGGT 59.839 42.308 0.00 0.00 36.34 3.08
1810 2553 6.607019 AGGTAGTCAGATAAACTCCTCTAGG 58.393 44.000 0.00 0.00 0.00 3.02
1811 2554 8.653191 TCTAGGTAGTCAGATAAACTCCTCTAG 58.347 40.741 0.00 0.00 31.28 2.43
1812 2555 8.564364 TCTAGGTAGTCAGATAAACTCCTCTA 57.436 38.462 0.00 0.00 31.28 2.43
1813 2556 7.420913 CCTCTAGGTAGTCAGATAAACTCCTCT 60.421 44.444 0.00 0.00 31.28 3.69
1814 2557 6.713450 CCTCTAGGTAGTCAGATAAACTCCTC 59.287 46.154 0.00 0.00 31.28 3.71
1815 2558 6.390461 TCCTCTAGGTAGTCAGATAAACTCCT 59.610 42.308 0.00 0.00 36.34 3.69
1816 2559 6.603224 TCCTCTAGGTAGTCAGATAAACTCC 58.397 44.000 0.00 0.00 36.34 3.85
1817 2560 7.284820 ACTCCTCTAGGTAGTCAGATAAACTC 58.715 42.308 0.00 0.00 36.34 3.01
1818 2561 7.215743 ACTCCTCTAGGTAGTCAGATAAACT 57.784 40.000 0.00 0.00 36.34 2.66
1819 2562 7.885009 AACTCCTCTAGGTAGTCAGATAAAC 57.115 40.000 0.00 0.00 36.34 2.01
1820 2563 7.894364 ACAAACTCCTCTAGGTAGTCAGATAAA 59.106 37.037 0.00 0.00 36.34 1.40
1821 2564 7.411808 ACAAACTCCTCTAGGTAGTCAGATAA 58.588 38.462 0.00 0.00 36.34 1.75
1822 2565 6.971340 ACAAACTCCTCTAGGTAGTCAGATA 58.029 40.000 0.00 0.00 36.34 1.98
1829 2572 4.263435 ACTCGACAAACTCCTCTAGGTAG 58.737 47.826 0.00 0.00 36.34 3.18
1845 2588 2.680352 TCCAGCCCCAGACTCGAC 60.680 66.667 0.00 0.00 0.00 4.20
1865 2608 5.684704 CCTTCCATAGATGCTTAAAGGACA 58.315 41.667 0.00 0.00 0.00 4.02
1866 2609 4.517075 GCCTTCCATAGATGCTTAAAGGAC 59.483 45.833 2.55 0.00 0.00 3.85
1868 2611 3.823304 GGCCTTCCATAGATGCTTAAAGG 59.177 47.826 0.00 0.00 0.00 3.11
1881 3206 1.312884 AAGGAATCCTGGCCTTCCAT 58.687 50.000 20.42 8.55 40.37 3.41
1904 3229 7.602644 GGATCAGATATAACCGCACTTTAATCA 59.397 37.037 0.00 0.00 0.00 2.57
1915 3770 2.029380 TGTGCCGGATCAGATATAACCG 60.029 50.000 5.05 0.00 42.67 4.44
1922 3777 2.711711 GCATTGTGCCGGATCAGAT 58.288 52.632 5.05 0.00 37.42 2.90
1923 3778 4.223800 GCATTGTGCCGGATCAGA 57.776 55.556 5.05 0.00 37.42 3.27
1940 3795 7.905604 TCCATATTATCTTTCGTAGCAATGG 57.094 36.000 0.00 0.00 0.00 3.16
1950 3805 9.173939 CATCTGCGTTTTTCCATATTATCTTTC 57.826 33.333 0.00 0.00 0.00 2.62
1969 3824 2.205074 GTAATCACCAGTCCATCTGCG 58.795 52.381 0.00 0.00 42.38 5.18
1973 3828 4.579869 ACAAGTGTAATCACCAGTCCATC 58.420 43.478 0.00 0.00 44.83 3.51
1975 3830 3.554129 CGACAAGTGTAATCACCAGTCCA 60.554 47.826 11.92 0.00 44.83 4.02
1977 3832 3.909430 TCGACAAGTGTAATCACCAGTC 58.091 45.455 9.25 9.25 44.83 3.51
2014 3869 9.282569 AGTAAAGAATAAATGATGGATGCTCTC 57.717 33.333 0.00 0.00 0.00 3.20
2039 5997 6.525628 CACATATAAAACAGCAGCAGAACAAG 59.474 38.462 0.00 0.00 0.00 3.16
2070 6028 2.703798 CCCAGAGCACGGCAAATGG 61.704 63.158 0.00 3.66 0.00 3.16
2071 6029 1.973281 ACCCAGAGCACGGCAAATG 60.973 57.895 0.00 0.00 0.00 2.32
2139 6109 2.556622 ACATGAAAGTTAAGGCCCAACG 59.443 45.455 0.00 0.00 0.00 4.10
2143 6113 2.231235 CCACACATGAAAGTTAAGGCCC 59.769 50.000 0.00 0.00 0.00 5.80
2148 6118 4.798924 GCAATGCCCACACATGAAAGTTAA 60.799 41.667 0.00 0.00 0.00 2.01
2154 6124 0.604073 CTGCAATGCCCACACATGAA 59.396 50.000 1.53 0.00 0.00 2.57
2173 6143 0.530431 CACAACACCCAGCAAAAGGC 60.530 55.000 0.00 0.00 45.30 4.35
2174 6144 0.104671 CCACAACACCCAGCAAAAGG 59.895 55.000 0.00 0.00 0.00 3.11
2175 6145 1.110442 TCCACAACACCCAGCAAAAG 58.890 50.000 0.00 0.00 0.00 2.27
2176 6146 1.561643 TTCCACAACACCCAGCAAAA 58.438 45.000 0.00 0.00 0.00 2.44
2177 6147 1.561643 TTTCCACAACACCCAGCAAA 58.438 45.000 0.00 0.00 0.00 3.68
2178 6148 1.205893 GTTTTCCACAACACCCAGCAA 59.794 47.619 0.00 0.00 0.00 3.91
2179 6149 0.820871 GTTTTCCACAACACCCAGCA 59.179 50.000 0.00 0.00 0.00 4.41
2180 6150 1.067060 GAGTTTTCCACAACACCCAGC 59.933 52.381 0.00 0.00 0.00 4.85
2181 6151 1.333619 CGAGTTTTCCACAACACCCAG 59.666 52.381 0.00 0.00 0.00 4.45
2182 6152 1.340211 ACGAGTTTTCCACAACACCCA 60.340 47.619 0.00 0.00 0.00 4.51
2183 6153 1.385528 ACGAGTTTTCCACAACACCC 58.614 50.000 0.00 0.00 0.00 4.61
2184 6154 4.823790 ATTACGAGTTTTCCACAACACC 57.176 40.909 0.00 0.00 0.00 4.16
2185 6155 6.617953 GCTCTATTACGAGTTTTCCACAACAC 60.618 42.308 0.00 0.00 33.55 3.32
2186 6156 5.407387 GCTCTATTACGAGTTTTCCACAACA 59.593 40.000 0.00 0.00 33.55 3.33
2187 6157 5.163884 GGCTCTATTACGAGTTTTCCACAAC 60.164 44.000 0.00 0.00 33.55 3.32
2193 6163 4.434520 AGCAGGCTCTATTACGAGTTTTC 58.565 43.478 0.00 0.00 33.55 2.29
2224 6194 6.328934 TCAACAGGGGCTGATATCAACTTATA 59.671 38.462 6.90 0.00 35.18 0.98
2225 6195 5.132648 TCAACAGGGGCTGATATCAACTTAT 59.867 40.000 6.90 0.00 35.18 1.73
2256 6226 4.259970 CGAAGGAAAGATCGCATGTAACAG 60.260 45.833 0.00 0.00 31.71 3.16
2266 6236 3.064207 TCCAAACACGAAGGAAAGATCG 58.936 45.455 0.00 0.00 44.33 3.69
2268 6238 3.815401 CTGTCCAAACACGAAGGAAAGAT 59.185 43.478 0.00 0.00 38.78 2.40
2269 6239 3.202906 CTGTCCAAACACGAAGGAAAGA 58.797 45.455 0.00 0.00 38.78 2.52
2287 6257 2.569059 CCGATCATTCTGCATTCCTGT 58.431 47.619 0.00 0.00 0.00 4.00
2367 6337 1.796190 AAGTCGTCTGCGCAGTCTCA 61.796 55.000 34.70 15.04 38.14 3.27
2371 6341 3.043419 AGAAGTCGTCTGCGCAGT 58.957 55.556 34.70 16.58 34.29 4.40
2380 6350 1.672356 GGCCATGCACAGAAGTCGT 60.672 57.895 0.00 0.00 0.00 4.34
2432 6402 1.594862 CTCATCGTTTTCCAGATCCGC 59.405 52.381 0.00 0.00 0.00 5.54
2434 6404 3.249559 GCATCTCATCGTTTTCCAGATCC 59.750 47.826 0.00 0.00 0.00 3.36
2443 6415 2.234661 TCACTCCAGCATCTCATCGTTT 59.765 45.455 0.00 0.00 0.00 3.60
2449 6421 1.274447 CACAGTCACTCCAGCATCTCA 59.726 52.381 0.00 0.00 0.00 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.